Align Phosphomannomutase/phosphoglucomutase; PMM / PGM; EC 5.4.2.2; EC 5.4.2.8 (uncharacterized)
to candidate WP_036259858.1 DL86_RS07610 phosphomannomutase/phosphoglucomutase
Query= curated2:Q88C93 (463 letters) >NCBI__GCF_000746085.1:WP_036259858.1 Length = 499 Score = 247 bits (631), Expect = 6e-70 Identities = 164/468 (35%), Positives = 245/468 (52%), Gaps = 24/468 (5%) Query: 14 FRAYDIRGVVGKTLHAETAYWIGRAIGAQSLAQG-EPQVSVGRDGRLSGPMLVEQLIKGL 72 FR YD R + K ++ +G +G G +P + G D R + L+ GL Sbjct: 27 FREYDARWIFEKEINLMGVQALGLGLGTLLHDLGVKPVLVTGHDFRAYSASIKYALMTGL 86 Query: 73 VDAGCNVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFKIVIAGD-TLANEQI 131 + AG V D+GL +P Y+A L + M+T SHN + + G K+ T +++ Sbjct: 87 MAAGVKVHDIGLALSPMAYFAQFELDVPAVAMVTASHNDNGWTGVKMGAQRPVTFGPDEM 146 Query: 132 QALLTRLKTNDLTLAQGRVEKV--EILDRYFKQIVGDVKLAKKLKVVVDCGNGAAGVVAP 189 + L + A G + + RY +V K+A+KLKVV CGNG AG AP Sbjct: 147 ERLKAIVLEGKFRYADGGSYRFVEDFPARYIADLVNRPKIARKLKVVAACGNGTAGAFAP 206 Query: 190 QLIEALGCEVIPLFCEVDGNFPNHHPDPGKPENLEDLIAKVKETGADIGLAFDGDGDRVG 249 +++E LGCEVIPL E+D FPN++P+P + L + KV+ETGAD+GL FDGDGDR G Sbjct: 207 KVLEKLGCEVIPLDAELDFTFPNYNPNPEDLKMLHAMADKVRETGADVGLGFDGDGDRCG 266 Query: 250 VVTNTGSIVYPDRLLMLFAQDVLSRNPGAEIIFDVKCTRRLT--PLIEQHGGRALMWKTG 307 VV N G ++ D++ ++ A+D+ P A + DVK T P + Q G +A WKTG Sbjct: 267 VVDNRGEEIFADKIGVMLARDLSKLYPNATFVVDVKSTGLFATDPQLLQQGVKADYWKTG 326 Query: 308 HSLIKKKMKQTGSLLAGEMSGHIFIKER-WYGFDDGIYSAARLLEILSKTE-QSAENLFA 365 HS IK+++ +L E SGH F G+DDGI +A ++E+L + +S L+ Sbjct: 327 HSYIKRRVTDLKALAGFEKSGHFFFNAPVGRGYDDGILTAIHVIEMLDRNPGKSMAELYD 386 Query: 366 AFPNDISTPEINIDVTDEGKFSIID-ALQRDADWGE----------ANLTTIDGVRVDYA 414 A P +P ++ DE K+ ++D + D E +L T++GVRV Sbjct: 387 ALPKTWGSPTMSPHCDDEKKYGVVDKVVGHFKDMQEKGRSLTGQKIRDLVTVNGVRVTVD 446 Query: 415 NG-WGLVRASNTTPVLVLRFEADSDAELQRIKDVFRT--QLLRVEPEL 459 +G WGLVRAS+ P LV+ E S R++++F +LR PE+ Sbjct: 447 DGTWGLVRASSNKPELVVVVE--SPVSEARMREMFAAVDAILRENPEV 492 Lambda K H 0.319 0.138 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 592 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 499 Length adjustment: 34 Effective length of query: 429 Effective length of database: 465 Effective search space: 199485 Effective search space used: 199485 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory